Evidence map›Paper›PMID 35982671›Full record

ArticleResearch square2022

Within-host diversity of SARS-CoV-2 lineages and effect of vaccination.

Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Daisy Y M Ng, Lydia D J Chang, Gigi Y Z Liu, Samuel S M Cheng, Tommy T Y Lam, Malik Peiris, Matthew R McKay and 1 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 2 countries.

Haogao GuSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.ORCID 0000-0002-7541-4262
Ahmed Abdul QuadeerDepartment of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.ORCID 0000-0002-5295-9067
Pavithra KrishnanSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Daisy Y M NgSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Lydia D J ChangSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Gigi Y Z LiuSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Samuel S M ChengSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Tommy T Y LamSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.ORCID 0000-0002-9769-1527
Malik PeirisSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.ORCID 0000-0001-8217-5995
Matthew R McKayDepartment of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
Leo L M PoonSchool of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.ORCID 0000-0002-9101-7953
University of Hong Kong · HKHong Kong Science and Technology Parks Corporation · HKHong Kong University of Science and Technology · HKThe University of Melbourne · AU

Funding

NIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00016 · NIAID · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI WEBBY, RICHARD · 2021 to 2025
$91.4M
Emerging infections: surveillance, epidemiology and pathogenesisU01AI151810 · NIAID · WASHINGTON UNIVERSITY · PI Adrianus CM Boon, DAVID WANG · 2020 to 2026
$10.0M
NIAID NIH HHS 75N93021C00016NIAID NIH HHS U01 AI151810
6 · The paper itself

Abstract

Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.

Identifiers

PMID35982671
PMCPMC9387541
OpenAlexW4293677330

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.